Publications

Year 2020


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Madrid-Gambin, Francisco, Oller-Moreno, Sergio, Fernandez, Luis, Bartova, Simona, Giner, Maria Pilar, Joyce, Christopher, Ferraro, Francesco, Montoliu, Ivan, Moco, Sofia, Marco, Santiago, (2020). AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics Bioinformatics revisar (no pdf) no en web general, revisar (no pdf) no en web general

NMR-based metabolomics is widely used to obtain metabolic fingerprints of biological systems. While targeted workflows require previous knowledge of metabolites, prior to statistical analysis, untargeted approaches remain a challenge. Computational tools dealing with fully untargeted NMR-based metabolomics are still scarce or not user-friendly. Therefore, we developed AlpsNMR (Automated spectraL Processing System for NMR), an R package that provides automated and efficient signal processing for untargeted NMR metabolomics. AlpsNMR includes spectra loading, metadata handling, automated outlier detection, spectra alignment and peak-picking, integration, and normalization. The resulting output can be used for further statistical analysis. AlpsNMR proved effective in detecting metabolite changes in a test case. The tool allows less experienced users to easily implement this workflow from spectra to a ready-to-use dataset in their routines.The AlpsNMR R package and tutorial is freely available to download from http://github.com/sipss/AlpsNMR under the MIT license.


Fabregas, R., Gomila, G., (2020). Dielectric nanotomography based on electrostatic force microscopy: A numerical analysis Journal of Applied Physics 127, (2), 024301

Electrostatic force microscopy (EFM) can image nanoscale objects buried below the surface. Here, we theoretically show that this capability can be used to obtain nanotomographic information, i.e., the physical dimensions and dielectric properties, of buried nano-objects. These results constitute a first step toward implementing a nondestructive dielectric nanotomography technique based on EFM with applications in materials sciences and life sciences.


Torner, M., Mangal, A., Scharnagl, H., Jansen, C., Praktiknjo, M., Queck, A., Gu, W., Schierwagen, R., Lehmann, J., Uschner, F. E., Graf, C., Strassburg, C. P., Fernandez, J., Stojakovic, T., Woitas, R., Trebicka, J., (2020). Sex specificity of kidney markers to assess prognosis in cirrhotic patients with TIPS Liver International 40, (1), 186-193

Background & Aims: Renal function assessed by creatinine is a key prognostic factor in cirrhotic patients. However, creatinine is influenced by several factors, rendering interpretation difficult in some situations. This is especially important in early stages of renal dysfunction where renal impairment might not be accompanied by an increase in creatinine. Other parameters, such as cystatin C (CysC) and beta‐trace protein (BTP), have been evaluated to fill this gap. However, none of these studies have considered the role of the patient's sex. The present study analysed CysC and BTP to evaluate their prognostic value and differentiate them according to sex. Patients and methods: CysC and BTP were measured in 173 transjugular intrahepatic portosystemic shunt (TIPS)-patients from the NEPTUN-STUDY(NCT03628807) and analysed their relationship with mortality and sex. Propensity score for age, MELD, etiology and TIPS indication was used. Results: Cystatin C and BTP showed excellent correlations with creatinine values at baseline and follow-up. CysC was an independent predictor of overall mortality (HR = 1.66(1.33-2.06)) with an AUC of 0.75 and identified a cut-off of 1.55 mg/L in the whole cohort. Interestingly, CysC was significantly lower in females, also after propensity score matching. In males, the only independent predictor was the creatinine level (HR = 1.54(1.25-1.58)), while in females CysC levels independently predicted mortality (HR = 3.17(1.34-7.52)). Conclusion: This study demonstrates for the first time that in TIPS-patients creatinine predicts mortality in males better than in females, whereas CysC is a better predictor of mortality in females. These results may influence future clinical decisions on therapeutic options for example, allocation for liver transplantation in TIPS-patients.

Keywords: Beta-trace protein, Cirrhosis, Cystatin C, Portal hypertension, Renal function


Puigbò, J. Y., Arsiwalla, X. D., González-Ballester, M. A., Verschure, P., (2020). Switching operation modes in the neocortex via cholinergic neuromodulation Molecular Neurobiology 57, (1), 139-149

In order to deal with the uncertainty in the world, our brains need to be able to flexibly switch between the exploration of new sensory representations and exploitation of previously acquired ones. This requires forming accurate estimations of what and how much something is expected. While modeling has allowed for the development of several ways to form predictions, how the brain could implement those is still under debate. Here, we recognize acetylcholine as one of the main neuromodulators driving learning based on uncertainty, promoting the exploration of new sensory representations. We identify its interactions with cortical inhibitory interneurons and derive a biophysically grounded computational model able to capture and learn from uncertainty. This model allows us to understand inhibition beyond gain control by suggesting that different interneuron subtypes either encode predictions or estimate their uncertainty, facilitating detection of unexpected cues. Moreover, we show how acetylcholine-like neuromodulation uniquely interacts with global and local sources of inhibition, disrupting perceptual certainty and promoting the rapid acquisition of new perceptual cues. Altogether, our model proposes that cortical acetylcholine favors sensory exploration over exploitation in a cortical microcircuit dedicated to estimating sensory uncertainty.


Blancas, Maria, Valero, Cristina, Mura, Anna, Vouloutsi, Vasiliki, Verschure, P., (2020). "CREA": An inquiry-based methodology to teach robotics to children Robotics in Education International Conference on Robotics in Education (RiE) , Springer International Publishing (Vienna, Austria) Advances in Intelligent Systems and Computing (AISC, volume 1023), 45-51

Learning programming and robotics offers the opportunity to practice problem-solving, creativity, and team-work and it provides important competencies to train for the 21st century. However, programming can be challenging, and children may encounter difficulties in learning the syntax or using the coding environment. To address this issue, we have developed a methodology for teaching programming, design and robotics based on inquiry-based learning and hands-on oriented activities together with visual programming. We have applied and evaluated this new methodology within the extracurricular activity of an international elementary school in Barcelona. Our findings showed acquisition and learning of technical language, understanding of electronics devices, understanding the mapping of coding into action via the robot’s behavior. This suggests that our approach is a valid and effective teaching methodology for the instructional design of robotics and programming.

Keywords: Educational technology, Instructional design, Robotics